By default, perltidy handles list with fat commas differently than plain lists. See "Controlling List Formatting" in the perltidy man page. This worked for me:

perltidy -st -cab=1 -mft=1 -lp -vt=1 -boc PM_503139_02.pl
[download]

Output:

my @list = ( '1',
             '2',
             '3',
);

my %hash = ( a => '1',
             b => '2',
             c => '3',
);
[download]

Key:

-boc     --break-at-old-comma-breakpoints
-mft=n   --maximum-fields-per-table=n
-cab=n   --comma-arrow-breakpoints=n
         
-lp      --line-up-parentheses
-pt=n    --paren-tightness=n
-vt=n    --vertical-tightness=n
-vtc=n   --vertical-tightness-closing=n
[download]

The real problem was in stopping @list from being flattened into one line, which perlytidy wants to do whenever the list *could* fit on a single line. The '-boc' flag, which tells it to using existing linebreaks, keeps @list in multi-line form, but this may be non-optimal for formatting the rest of your program.